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Biomolecular Mass Spectrometry
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Members
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Main topics
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The research activities of this group are situated in the field of the study of the interaction of alkylating xenobiotics with DNA. These molecules induce changes in DNA because of the formation of so-called DNA-adducts. It is generally believed that these adducts are responsible for the initial tumour formation. Modified nucleos(t)ide material is investigated with the aid of electrospray mass spectrometry and electrospray tandem mass spectrometry in combination with capillary- and nano-HPLC. These sophisticated and innovative techniques are also used in combination with enzymatic procedures used for sample preparation. The analytical system is combined with an on-line column switching system allowing the enrichment of modified nucleos(t)ide material. Modifications are also investigated in oligonucleotides, cell cultures and tumour tissue. Target xenobiotics are Melphalan and estrogens. Other topics are the development of LC-MS methods for the analysis of nucleoside mono- di- and triphosphates and the analysis of modified nucleosides in urine samples of cancer patients as early biomarkers. This is done in collaboration with Prof.R.Newton (University of Wales, Swansea, UK), in collaboration with Prof.M.Tornqvist and Dr.J.Haglund and as a partner in an EU research & training network. LC-MS analyses of cobalamins are also carried out. The group also collaborates with the groups of plant physiology (Prof. Van Onckelen), protein chemistry (prof. L. Moens) and ecotoxicology (Profs. R. Blust & W. De Coen). The research group also participates in the centre of mass spectrometry & proteomics.
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Website
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http://aether.cmi.ua.ac.be/researchgroup/research.htm
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Projects
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Show the projects of this research team - 4D Protein Structure. 01/01/2013 - 31/12/2016
| Abstract | In our research we will investigate two recent, complementary biophysical approaches, ''native'' ion mobility/mass spectrometry (IM-MS) and Vibrational Optical Activity (VOA), to investigate structure and dynamics of proteins of biomedical interest. Specifically we will benchmark these techniques against well-studied protein systems, and apply them to probe changes in the conformational and assembly space of globins and oligopeptidases. | | Duration | 01/01/2013 - 31/12/2016 | | Researcher(s) | | | Research Team(s) | |
- No title found 01/01/2013 - 31/12/2013
| Abstract | One of the most fundamental biological processes is the ability of a cell to facilitate the selective movement of ions and small molecules across the plasma membrane; this allows a cell to interact with its environment. The rapid movement of inorganic ions such as Na+, K+, Ca2+ and Cl- across the membrane in response to electrochemical gradients is achieved by ion channels: integral membrane proteins that provide ion-selective pathways across the otherwise impermeable cell membrane. However, ion channels are not simply unregulated pores.
Instead, they are "gated", i.e. they open and close in response to a variety of mechanical, thermal, electrical and chemical signals. The inwardly rectifying potassium (Kir) channels comprise a superfamily of K+ channels that regulate membrane electrical excitability and K+ transport in many cell types. Kir channels are found in almost every cell in the body where they control such diverse processes as heart rate, vascular tone, insulin secretion and salt/fluid balance. | | Duration | 01/01/2013 - 31/12/2013 | | Researcher(s) | | | Research Team(s) | |
- Developoing new tools for (un)structural biology by ion mobility-mass spectrometry and related methods. 01/10/2012 - 31/01/2016
| Abstract | In our research we will use state-of-the-art ''native'' mass spectrometric techniques to investi-gate both the dynamic as well as structural characteristics of membrane (associated) proteins. Furthermore will we probe the changes in conformational space of proteins when they interact with ligand or other proteins using ion mobility-mass spectrometry, with a special focus on intrinsically disordered proteins.F2016r | | Duration | 01/10/2012 - 31/01/2016 | | Researcher(s) | | | Research Team(s) | |
- Development and application of novel proteomics methods. 01/10/2012 - 30/09/2014
| Abstract | We propose to develop MS-based analytical techniques, to be used in proteomics research. We will subsequently
use these techniques to investigate the structure of proteins and other biopolymers. | | Duration | 01/10/2012 - 30/09/2014 | | Researcher(s) | | | Research Team(s) | |
- Analysis of protein/nucleic acid complexes by native ion mobility mass spectrometry. 01/10/2012 - 30/09/2013
| Abstract | The goal of the project is to analyze the composition, stoichiometry, overall 3D structure and function of nucleic acids and associated protein complexes that play important roles in processes that control the organization and regulation of the genome (e.g. cell division
and gene expression). This will help to understand fundamental biological processes and diseases on the molecular level which are related to cell growth and cell division (e.g. stem cell development, aging or cancer). | | Duration | 01/10/2012 - 30/09/2013 | | Researcher(s) | | | Research Team(s) | |
- Generation of 2nd generation mannosylerythritol lipids (MEL's) using fermentation technology and the further design of these MEL's for use in cosmetic applications. 01/09/2012 - 31/08/2016
| Abstract | This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract. | | Duration | 01/09/2012 - 31/08/2016 | | Researcher(s) | | | Research Team(s) | |
- Analysis of mannosyl erythritol lipid biosurfactants and screening of specific antimicrobial activities (BACTIMEL). 01/01/2012 - 31/12/2013
| Abstract | Complex mixtures of mannosyl erythritol lipid (MEL) biosurfactants produced via fermentation will be purified and analytically characterized by liquid chromatography and mass spectrometry. The pure compounds will be screened for their activity against bacteria and fungi. | | Duration | 01/01/2012 - 31/12/2013 | | Researcher(s) | | | Research Team(s) | |
- Developing a global understanding of the PRC and NuRD complexes in stemm cell differentiation, in health and disease (4DCellfate). 01/12/2011 - 30/11/2016
| Abstract | The goal of 4DCellFate is to understand how the PRC/NuRD complexes and their plethora of interactions
(protein/protein, protein/nucleosome, protein/nucleic acids) regulate cell fate. The ultimate outcome of 4DCellFate will be to lay the foundations for understanding the role of the PRC/NuRD complexes in ES cell differentiation and cancer, specifically in leukaemogenesis. | | Duration | 01/12/2011 - 30/11/2016 | | Researcher(s) | | | Research Team(s) | |
- Identification of degradation products of coated proteins on teflon. 01/12/2011 - 30/11/2012
| Abstract | This project represents a formal service agreement between UA and on the other hand Anethon. UA provides Anethon research results mentioned in the title of the project under the conditions as stipulated in this contract. | | Duration | 01/12/2011 - 30/11/2012 | | Researcher(s) | | | Research Team(s) | |
- Development and application of novel proteomics methods. 03/10/2011 - 02/10/2015
| Abstract | There is a gap between the importance of PTM''s and the technology available to study PTMs in a high-throughput fashion. The purpose of this project is to bridge this by developing and applying novel proteomics approaches based on ion mobility spectrometry (IMS) and electron transfer dissociation (ETD) on two state-of-the-art platforms, a Water Synapt G2 with ETD and a Thermo Orbitrap Velos with FAIMS and ETD. | | Duration | 03/10/2011 - 02/10/2015 | | Researcher(s) | | | Research Team(s) | |
- Francqui research professor "Mass Spectrometry". 01/09/2011 - 31/08/2014
| Abstract | This project represents a formal research agreement between UA and on the other hand a private institution. UA provides the private institution research results mentioned in the title of the project under the conditions as stipulated in this contract. | | Duration | 01/09/2011 - 31/08/2014 | | Researcher(s) | | | Research Team(s) | |
- Towards a new dimension in mass spectrometry: Characterisation of components, assembly, topology and function of molecular machines for DNA processing. 01/01/2011 - 31/12/2014
| Abstract | We aim to understand how genetic information, stored as a specific DNA sequence, is organized, maintained and read out by the protein machinery of living cells. In many organisms ranging from bacteria to humans, specific and highly regulated complexes of protein molecules form ring-like structures as large as 50 nanometers in diameter to bring together or hold two related chromosomes (sister chromatids), and allow their controlled release into the opposite halves of the dividing cell. This process is crucial for cell division and survival, and is regulated by the (dis)assembly of complexes of SMC proteins (Structural Maintenance of Chromosomes) and their associated proteins.
To gain insight into the formation and dissociation of these protein assemblies and investigate their structure, we are developing new methods based on mass spectrometric detection of intact, isolated complexes in the gas phase and study their shape and size using a novel adjunct method, ion mobility spectroscopy. This will enable a better understanding of how the proteins recognize DNA, form specific arrangements of subunits and cofactors and how they perform their function as DNA-processing "machines". | | Duration | 01/01/2011 - 31/12/2014 | | Researcher(s) | | | Research Team(s) | |
- Ion mobility high resolution mass spectrometer: a strong tool for fragile structures. 22/07/2010 - 21/07/2015
| Abstract | This project has two general objectives:
(1) Increase the research potential of the UA by introduction of new state of the art techniques for the analysis of fragile molecular structures by using the novel ion mobility capabilities that have recently been integrated with high-mass high-resolution Q-TOF mass spetrometry ("Synapt", waters).
(2) Maintain the current capacity to obtain Q-TOF data by replacing an existing system. | | Duration | 22/07/2010 - 21/07/2015 | | Researcher(s) | | | Research Team(s) | |
- Analytical characterisation of mannosylerythritol lipid biosurfactants produced by biosynthesis based on feedstock sources from agro-food industry. 01/01/2010 - 31/12/2011
| Abstract | A fermentation based on feedstock sources from agro-food industry for the production of mannosylerythritol lipid biosurfactants (BIOMEL project) yields in a secretion of a complex blend of biomolecules with promising properties in food-, pharmaceutical, cosmetic and domestic housecare applications. The goal of this project is to define detailed protocols of standard procedures for isolation, purification, quantification and characterisation of current and novel MEL''s from a complete fermentation broth. | | Duration | 01/01/2010 - 31/12/2011 | | Researcher(s) | | | Research Team(s) | |
- Determination of subunit composition and architecture of supramolecular and biological complexes using mass spectrometry coupled with ion mobility spectroscopy and allied techniques. 01/11/2009 - 31/10/2014
| Abstract | We are developing and applying new methods for the intact characterisation of supramolecular systems, particularly noncovalent complexes of biomolecules (proteins, DNA/RNA and ligands), based on soft ionisation techniques such as electrospray ionisation and laser desorption methods, coupled with mass spectrometry and ion mobility spectroscopy. Extensive collaboration with colleagues in the areas of Biochemistry and Chemistry are envisaged. | | Duration | 01/11/2009 - 31/10/2014 | | Researcher(s) | | | Research Team(s) | |
- Towards a new dimension of mass spectrometry. 01/11/2009 - 31/10/2014
| Abstract | We are developing and applying new methods for the intact characterisation of supramolecular systems, particularly noncovalent complexes of biomolecules (proteins, DNA/RNA and ligands), based on soft ionisation techniques such as electrospray ionisation and laser desorption methods, coupled with mass spectrometry and ion mobility spectroscopy. Extensive collaboration with colleagues in the areas of Biochemistry and Chemistry are envisaged. | | Duration | 01/11/2009 - 31/10/2014 | | Researcher(s) | | | Research Team(s) | |
- Influence of melphalan isolated lung perfusion on the (phospho)-proteome. 01/07/2009 - 31/12/2013
| Abstract | This project studies the regulation, phosphorylation and adduct formation of proteins in tumors upon melphalan treatment. LC-MS methods will be developed using a representative cell culture. An animal model (induced lung tumors) will be treated by melphalan isolated lung perfusion prior to analysis of human samples. Final goal is the selection of candidate biomarkers ((phospho-)protein, melphalan-proteinadduct, ...) with prognostic value for the treatment of lung metastases by melphalan-ILuP. | | Duration | 01/07/2009 - 31/12/2013 | | Researcher(s) | | | Research Team(s) | |
- A high-resolution mass spectrometry and electron microscopy approach to understanding the function of the Shigella T3SS. 01/06/2009 - 30/11/2012
| Abstract | This project represents a formal research agreement between UA and on the other hand University of Bristol. UA provides University of Bristol research results mentioned in the title of the project under the conditions as stipulated in this contract. | | Duration | 01/06/2009 - 30/11/2012 | | Researcher(s) | | | Research Team(s) | |
- Study on the use of melphalan-DNA adducts as biomarkers in isolated lung perfusions: qualitative-quantitative analysis of DNA formed adducts . 23/09/2008 - 31/12/2010
| Abstract | No abstract found | | Duration | 23/09/2008 - 31/12/2010 | | Researcher(s) | | | Research Team(s) | |
- Development and optimization of the analysis of perfluoralkyl compounds in selected food matrices. 01/01/2007 - 31/12/2007
| Abstract | No abstract found | | Duration | 01/01/2007 - 31/12/2007 | | Researcher(s) | | | Research Team(s) | |
- The integration of an Arabidopsis TAP dataset into a cell cycle related protein interaction network. 01/10/2006 - 30/09/2008
| Abstract | No abstract found | | Duration | 01/10/2006 - 30/09/2008 | | Researcher(s) | | | Research Team(s) | |
- CEPROMA: Centre for proteome analysis. Supporting core facilities. 01/09/2015 - 31/12/2016
| Abstract | This project represents a research contract awarded by the University of Antwerp. The supervisor provides the Antwerp University research mentioned in the title of the project under the conditions stipulated by the university. | | Duration | 01/09/2015 - 31/12/2016 | | Researcher(s) | | | Research Team(s) | |
- Proteome analysis of biotenside synthesis in yeast. 01/10/2006 - 31/12/2007
| Abstract | Using a proteomics based phenotyping strategy the metabolic profiling of a fermentation reaction will be investigated. For this purpose Candida bombicola is used as a model for the fermentation of renewable vegetable oils and the production of sophorolipids. By optimizing the culture parameters the production will be correlated with the phenotype with the aim to select a strain suitable for industrial fermentation. | | Duration | 01/10/2006 - 31/12/2007 | | Researcher(s) | | | Research Team(s) | |
- Support maintenance scientific equipment. 01/01/2005 - 31/12/2013
| Abstract | No abstract found | | Duration | 01/01/2005 - 31/12/2013 | | Researcher(s) | | | Research Team(s) | |
- A research initiative on the isolation and characterisation of biotensides obtained through fermentation of recycled oils and fats. 01/01/2005 - 31/12/2006
| Abstract | Sophorolipids (SL), synthesised from microorganism with various substrates, stand out as biosur-factants with a wide potential for industrial application. It is highly desirable to develop an efficient and consistent analytical platform for the separation, identification and quantification of the different SL components of the complex fermentation mixture, through LC-MSn. Special attention is stressed to the changes of SL composition with different supplied lipophilic substrates. | | Duration | 01/01/2005 - 31/12/2006 | | Researcher(s) | | | Research Team(s) | |
- An integrated Fourier- Transform mass spectrometer (FTMS). 01/12/2004 - 30/11/2007
| Abstract | No abstract found | | Duration | 01/12/2004 - 30/11/2007 | | Researcher(s) | | | Research Team(s) | |
- Development of new analytical methods for the determination of urinary nucleosides and nucleoside mono-, di-, and triphosphates, by means of a miniaturised HPLC-ESMS. 01/01/2004 - 31/12/2005
| Abstract | A: Urinary nucleosides
It is known that some modified nucleosides originating from RNA degradation are excreted in abnormal levels in the urine of patients with malignant tumours and they have been proposed as tumour markers. Their measurement could provide a non-invasive diagnostic method, helpful for the identification of different cancers and in the monitoring of therapeutic effects.
In this work the development of a fast on-line multi-column HPLC-ESMS(/MS) system for the selective sample clean up, preconcentration and subsequent analysis of the major and minor (modified) ribonucleosides in human urine will be the main objective. The high sensitivity and selectivity of miniaturised LC-MS(/MS) methods will provide us the means to isolate and detect unknown nucleosides. For the structure elucidation of those compounds MS/MS spectra will be generated and subsequently interpreted. If necessary further (spectroscopic) steps will be undertaken to offer assurance about the proposed structures.
As the proposed analytical method tolerates direct administration of urine samples, it opens the opportunity for a relatively fast screening of samples. So we will use the method to generate urinary nucleoside patterns of both healthy volunteers and cancerpatients. Those patterns will be evaluated in order to discriminate, based on nucleoside concentrations, between healthy men and those suffering from ovarian, prostate or abdominal cancer.
B: nucleotides
A lot of nucleoside-analogues, which are intracellular metabolized to active nucleotide-analogues, are used as antiviral and cytostatic therapeutics. Therefore higher demands are placed on the technology for the analysis of nucleotides. In addition to this it may be necessary for studies of cell metabolism to separate, determine and quantify mixtures of nucleoside mono-, di- and triphosphates. A lot of chromatographic procedures for the analysis of nucleotides -all based on UV or radiometric detection- were developed in the past. However in order to acquire highly selective structural information the development of a sensitive HPLC-MS(/MS) system is required. Due to the incompatibility of mass spectrometry with the originally proposed separation methods, the development of new LC-MS compatible separations was warranted. Ion-suppression HPLC (-) ESMS and ion-pair HPLC (-) ESMS have been used for the analysis of selected analytes. Yet, a more universally applicable analytical procedure would be useful for future studies concerning the purity and biochemical/medical behaviour of nucleotide-analogues. Special concern will go to a selective on-line sample clean up and preconcentration of the nucleotides. The use of a miniaturized LC-ESMS system equipped with a column-switching technique will result in an amplified mass and concentration sensitivity. | | Duration | 01/01/2004 - 31/12/2005 | | Researcher(s) | | | Research Team(s) | |
- Investigation of the "in vivo" interaction of melphalan with DNA with miniaturized liquid chromatography coupled to electrospray tandem mass spectrometry. 01/01/2004 - 31/12/2005
| Abstract | Chemotherapeutic compounds used in the treatment of cancer reduce tumoral cell growth by interacting with different biomolecules. As such they disturb or block cell replication.
One of these compounds, melphalan (L-phenylalanine mustard, 4-(bis(2-chloroethyl)amino)-L-phenylalanine, is a bifunctional alkylating agent that covalently binds to the nucleophilic sites present in DNA. In this study the interaction of melphalan is studied with DNA in ''in vivo'' experiments. Furhtermore the interaction of melphalan is studied with oligonucleotides with known sequence. | | Duration | 01/01/2004 - 31/12/2005 | | Researcher(s) | | | Research Team(s) | |
- Development and implementation of the interconnection of microfluidic devices and mass spectrometry. 01/10/2003 - 31/12/2005
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2005 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- A multidisciplinary study of oxygen-related stress phenomena, using advanced proteome analyses. 01/10/2003 - 31/12/2006
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2006 | | Researcher(s) | | | Research Team(s) | |
- Identification and characterization of proteins by means of mass spectrometry: proteome analysis. 01/10/2003 - 31/12/2006
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2006 | | Researcher(s) | | | Research Team(s) | |
- Cobalamin and Mimics. 01/10/2003 - 31/08/2005
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/08/2005 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 30/09/2004
| Abstract | No abstract found | | Duration | 01/10/2003 - 30/09/2004 | | Researcher(s) | | | Research Team(s) | |
- Functional proteome analysis. 01/10/2003 - 31/12/2006
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2006 | | Researcher(s) | | | Research Team(s) | |
- Study of the cAMP dependent induction of differentiation in rat C6 glioma. 01/10/2003 - 31/12/2005
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2005 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- 01/10/2003 - 31/12/2003
| Abstract | No abstract found | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
- Analysis and structure determination of biomolecules by direct coupling of nano-HPLC to nano-electrospray tandem mass spectrometry. 01/10/2003 - 31/12/2003
| Abstract | Development of a methodology based on nano-technology ( on-line column switching -nano HPLC -nanospray ES MS/MS ) for the "in vivo" measurements of DNA-adducts of patients treated in the hospital with Melphalan? and the study of adduct formation between estrogen-metabolites and DNA with the final aim the detection of estrogen -adducts in breast cancer tissue. These two topics are investigated in order to see which Melphalan adducts are formed and whether they are responsible for the development of secondary leukemia and to investigate which and how much estrogen adducts are found to study the effect of these adducts in the development of breast cancer in women taking additional doses of estrogens.
* Identification and quantitation of components of the signal transduction chain in higher plants , more in particular : proteins, auxins, cytokinins and gibberilines using both capillary HPLC and nano HPLC -approaches in order to get a better insight in plant metabolism..
* Study of proteins involved in Alzheimer disease and of proteins present in thermophylic organisms | | Duration | 01/10/2003 - 31/12/2003 | | Researcher(s) | | | Research Team(s) | |
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